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Étude Des Profils De Méthylation Et D'expression Des Lymphocytes T CD4+ Dans L'asthme

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Étude Des Profils De Méthylation Et D'expression Des Lymphocytes T CD4+ Dans L'asthme Étude des profils de méthylation et d'expression des lymphocytes T CD4+ dans l'asthme Mémoire Anne-Marie Boucher-Lafleur Maîtrise en sciences cliniques et biomédicales - avec mémoire de l’Université Laval offert en extension à l’Université du Québec à Chicoutimi Maître ès sciences (M. Sc.) Université du Québec à Chicoutimi Chicoutimi, Canada Médecine Université Laval Québec, Canada © Anne-Marie Boucher-Lafleur, 2019 Étude des profils de méthylation et d’expression des lymphocytes T CD4+ dans l’asthme Mémoire Anne-Marie Boucher-Lafleur Sous la direction de : Catherine Laprise, directrice de recherche RÉSUMÉ L’asthme est une maladie respiratoire chronique impliquant de l’inflammation, de l’hyperréactivité bronchique et un remodelage des voies respiratoires. Il s’agit d’un trait complexe résultant d’interactions entre des facteurs génétiques et environnementaux. La portion génétique de l’asthme a été bien décrite, avec une héritabilité estimée jusqu’à 60% selon les études. Une portion de l’héritabilité manquante dans l’asthme pourrait être expliquée par des facteurs épigénétiques, comme la méthylation de l’ADN. Comme la méthylation est spécifique à chaque tissu, il est logique d’étudier des cellules ayant un rôle important dans l’asthme. C’est le cas des lymphocytes T CD4+ qui contribuent activement à la pathophysiologie de l’asthme. L’objectif du présent projet était donc d’étudier les lymphocytes T CD4+ dans un contexte d’asthme, plus particulièrement leur patron de méthylation ainsi que leur patron d’expression. Ces lymphocytes ont été isolés du sang de plus de 200 individus faisant partie de la Cohorte familiale d’asthme du Saguenay–Lac-Saint-Jean. La méthylation et l’expression a ensuite été mesurée par séquençage. Après des contrôles de qualité, des données étaient disponibles pour 173 individus (107 asthmatiques, 66 témoins). Il a ainsi été possible d’identifier 2 146 sites CpG différemment méthylés chez les asthmatiques et 3 756 chez les asthmatiques allergiques (FDR≤0,05, -meth ≥ 5%). Pour l’expression, 57 et 33 gènes sont différemment exprimés chez les asthmatiques et les asthmatiques allergiques, respectivement (FDR≤0,05). L’intégration des données génétique et d’expression ont permis d’identifier 2 253 eQTL significatifs (FDR≤0,049). Ces résultats ont permis d’identifier l’implication de la voie de NF-B ainsi que celle de l’IL-17 et -25 dans ces cellules, mais aussi l’implication de la famille de chemokine CXC et de EGF. En somme, cette étude a permis de caractériser plus précisément un type cellulaire dans l’asthme, toujours dans le but de mieux comprendre les mécanismes sous-jacents impliqués dans cette condition. ii TABLE DES MATIÈRES RÉSUMÉ ............................................................................................................................................................. ii TABLE DES MATIÈRES ..................................................................................................................................... iii LISTE DES FIGURES .......................................................................................................................................... v LISTE DES TABLEAUX ...................................................................................................................................... vi LISTE DES ABRÉVIATIONS ............................................................................................................................. vii REMERCIEMENTS ............................................................................................................................................ xi INTRODUCTION ................................................................................................................................................ 1 1. Asthme................................................................................................................................................... 1 1.1 Épidémiologie....................................................................................................................................... 1 1.2 Phénotypes .......................................................................................................................................... 2 1.3 Physiopathologie .................................................................................................................................. 3 1.3.1 Sensibilisation à un allergène ....................................................................................................... 3 1.3.2 Phase précoce de l’inflammation .................................................................................................. 6 1.3.2.1 L’épithélium bronchique......................................................................................................... 6 1.3.2.2 Réexposition .......................................................................................................................... 6 1.3.3 Phase tardive de l’inflammation .................................................................................................... 8 1.3.3.1 Lymphocytes T CD4+ ............................................................................................................ 8 1.3.3.2 Éosinophiles et neutrophiles ................................................................................................ 11 1.3.4 Le remodelage des voies respiratoires ....................................................................................... 12 2. Composante génétique ............................................................................................................................ 15 3. Composante environnementale ................................................................................................................ 18 3.1 Épigénétique ...................................................................................................................................... 18 3.1.1 Méthylation de l’ADN .................................................................................................................. 20 3.3 Facteurs de risque ............................................................................................................................. 21 3.3.1 Âge et sexe ................................................................................................................................. 22 3.3.2 Obésité ....................................................................................................................................... 23 3.3.3 Qualité de l’air ............................................................................................................................. 23 3.3.4 Tabagisme .................................................................................................................................. 25 4. Population à l’étude .................................................................................................................................. 25 4.1 Historique ........................................................................................................................................... 25 4.2 La cohorte familiale d’asthme du Saguenay−Lac-Saint-Jean ............................................................ 27 5. Hypothèse et objectifs .............................................................................................................................. 29 CHAPITRE 1 – MÉTHODOLOGIE ................................................................................................................... 30 1.1 Recrutement des participants............................................................................................................. 30 1.2 Isolation des lymphocytes T CD4+ ..................................................................................................... 30 1.3 Données de méthylation .................................................................................................................... 32 1.3.1 Séquençage (MCC-seq) ............................................................................................................. 32 1.3.2 Alignement et contrôles qualités ................................................................................................. 34 1.4 Données d’expression ........................................................................................................................ 35 1.4.1 Séquençage de l’ARN ................................................................................................................ 35 1.4.2 Alignement et contrôles qualités ................................................................................................. 37 1.5 Données génétiques .......................................................................................................................... 38 1.6 Analyses ............................................................................................................................................. 38 1.6.1 Méthylation ................................................................................................................................. 38 1.6.2 Expression .................................................................................................................................. 40 1.6.3 Corrélations méthylation – expression ........................................................................................ 40 1.6.4 eQTL ..........................................................................................................................................
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